import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
{
- PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+ // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+ PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+ files[i]);
pdbentrys[i] = pdbentry;
}
// / TODO: check if protocol is needed to be set, and if chains are
}
try
{
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry(
- pi)
- .getId());
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
{
// just transfer the file name from the first sequence's first
// PDBEntry
- file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile()).getAbsolutePath();
+ file = new File(pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
files.append(" \"" + Platform.escapeString(file) + "\"");
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try
{
- for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++)
- {
- cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile()));
- cap.appendText("\n");
- }
+ cap.appendText(jmb.printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
getSize(currentSize);
g.getClipBounds(rectClip);
- if (jmb.fileLoadingError != null)
+ if (jmb != null && jmb.fileLoadingError != null)
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
return jmb == null ? null : jmb.viewer.getStateInfo();
}
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
}